1
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Lan T, Ganapathy US, Sharma S, Ahn Y, Zimmerman M, Molodtsov V, Hegde P, Gengenbacher M, Ebright RH, Dartois V, Freundlich JS, Dick T, Aldrich CC. Redesign of Rifamycin Antibiotics to Overcome ADP-Ribosylation-Mediated Resistance. Angew Chem Int Ed Engl 2022; 61:e202211498. [PMID: 36222275 PMCID: PMC9633546 DOI: 10.1002/anie.202211498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Indexed: 11/11/2022]
Abstract
Rifamycin antibiotics are a valuable class of antimicrobials for treating infections by mycobacteria and other persistent bacteria owing to their potent bactericidal activity against replicating and non-replicating pathogens. However, the clinical utility of rifamycins against Mycobacterium abscessus is seriously compromised by a novel resistance mechanism, namely, rifamycin inactivation by ADP-ribosylation. Using a structure-based approach, we rationally redesign rifamycins through strategic modification of the ansa-chain to block ADP-ribosylation while preserving on-target activity. Validated by a combination of biochemical, structural, and microbiological studies, the most potent analogs overcome ADP-ribosylation, restored their intrinsic low nanomolar activity and demonstrated significant in vivo antibacterial efficacy. Further optimization by tuning drug disposition properties afforded a preclinical candidate with remarkable potency and an outstanding pharmacokinetic profile.
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Affiliation(s)
- Tian Lan
- Department of Medicinal ChemistryCollege of PharmacyUniversity of Minnesota308 SE Harvard St SEMinneapolisMN 55455USA
| | - Uday S. Ganapathy
- Center for Discovery and InnovationHackensack Meridian Health & Department of Medical SciencesHackensack Meridian School of Medicine123 Metro BoulevardNutleyNJ 07110USA
| | - Sachin Sharma
- Department of Medicinal ChemistryCollege of PharmacyUniversity of Minnesota308 SE Harvard St SEMinneapolisMN 55455USA
| | - Yong‐Mo Ahn
- Department of Pharmacology and PhysiologyDepartment of MedicineCenter for Emerging and Reemerging PathogensRutgers University185 South Orange AvenueNewarkNJ 07103USA,National Center for Advancing Translational SciencesNational Institutes of HealthRockvilleMD 20850USA
| | - Matthew Zimmerman
- Center for Discovery and InnovationHackensack Meridian Health & Department of Medical SciencesHackensack Meridian School of Medicine123 Metro BoulevardNutleyNJ 07110USA
| | - Vadim Molodtsov
- Waksman InstituteRutgers University190 Frelinghuysen RoadPiscatawayNJ 08854USA
| | - Pooja Hegde
- Department of Medicinal ChemistryCollege of PharmacyUniversity of Minnesota308 SE Harvard St SEMinneapolisMN 55455USA
| | - Martin Gengenbacher
- Center for Discovery and InnovationHackensack Meridian Health & Department of Medical SciencesHackensack Meridian School of Medicine123 Metro BoulevardNutleyNJ 07110USA
| | - Richard H. Ebright
- Waksman InstituteRutgers University190 Frelinghuysen RoadPiscatawayNJ 08854USA
| | - Véronique Dartois
- Center for Discovery and InnovationHackensack Meridian Health & Department of Medical SciencesHackensack Meridian School of Medicine123 Metro BoulevardNutleyNJ 07110USA
| | - Joel S. Freundlich
- Department of Pharmacology and PhysiologyDepartment of MedicineCenter for Emerging and Reemerging PathogensRutgers University185 South Orange AvenueNewarkNJ 07103USA
| | - Thomas Dick
- Center for Discovery and InnovationHackensack Meridian Health & Department of Medical SciencesHackensack Meridian School of Medicine123 Metro BoulevardNutleyNJ 07110USA,Department of Microbiology and ImmunologyGeorgetown University3900 Reservoir Road NWWashingtonDC 20007USA
| | - Courtney C. Aldrich
- Department of Medicinal ChemistryCollege of PharmacyUniversity of Minnesota308 SE Harvard St SEMinneapolisMN 55455USA
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2
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Lan T, Ganapathy US, Sharma S, Ahn Y, Zimmerman M, Molodtsov V, Hegde P, Gengenbacher M, Ebright RH, Dartois V, Freundlich JS, Dick T, Aldrich CC. Redesign of Rifamycin Antibiotics to Overcome ADP‐Ribosylation‐Mediated Resistance. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202211498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Tian Lan
- Department of Medicinal Chemistry College of Pharmacy University of Minnesota 308 SE Harvard St SE Minneapolis MN 55455 USA
| | - Uday S. Ganapathy
- Center for Discovery and Innovation Hackensack Meridian Health & Department of Medical Sciences Hackensack Meridian School of Medicine 123 Metro Boulevard Nutley NJ 07110 USA
| | - Sachin Sharma
- Department of Medicinal Chemistry College of Pharmacy University of Minnesota 308 SE Harvard St SE Minneapolis MN 55455 USA
| | - Yong‐Mo Ahn
- Department of Pharmacology and Physiology Department of Medicine Center for Emerging and Reemerging Pathogens Rutgers University 185 South Orange Avenue Newark NJ 07103 USA
- National Center for Advancing Translational Sciences National Institutes of Health Rockville MD 20850 USA
| | - Matthew Zimmerman
- Center for Discovery and Innovation Hackensack Meridian Health & Department of Medical Sciences Hackensack Meridian School of Medicine 123 Metro Boulevard Nutley NJ 07110 USA
| | - Vadim Molodtsov
- Waksman Institute Rutgers University 190 Frelinghuysen Road Piscataway NJ 08854 USA
| | - Pooja Hegde
- Department of Medicinal Chemistry College of Pharmacy University of Minnesota 308 SE Harvard St SE Minneapolis MN 55455 USA
| | - Martin Gengenbacher
- Center for Discovery and Innovation Hackensack Meridian Health & Department of Medical Sciences Hackensack Meridian School of Medicine 123 Metro Boulevard Nutley NJ 07110 USA
| | - Richard H. Ebright
- Waksman Institute Rutgers University 190 Frelinghuysen Road Piscataway NJ 08854 USA
| | - Véronique Dartois
- Center for Discovery and Innovation Hackensack Meridian Health & Department of Medical Sciences Hackensack Meridian School of Medicine 123 Metro Boulevard Nutley NJ 07110 USA
| | - Joel S. Freundlich
- Department of Pharmacology and Physiology Department of Medicine Center for Emerging and Reemerging Pathogens Rutgers University 185 South Orange Avenue Newark NJ 07103 USA
| | - Thomas Dick
- Center for Discovery and Innovation Hackensack Meridian Health & Department of Medical Sciences Hackensack Meridian School of Medicine 123 Metro Boulevard Nutley NJ 07110 USA
- Department of Microbiology and Immunology Georgetown University 3900 Reservoir Road NW Washington DC 20007 USA
| | - Courtney C. Aldrich
- Department of Medicinal Chemistry College of Pharmacy University of Minnesota 308 SE Harvard St SE Minneapolis MN 55455 USA
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3
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Paulowski L, Beckham KSH, Johansen MD, Berneking L, Van N, Degefu Y, Staack S, Sotomayor FV, Asar L, Rohde H, Aldridge BB, Aepfelbacher M, Parret A, Wilmanns M, Kremer L, Combrink K, Maurer FP. C25-modified rifamycin derivatives with improved activity against Mycobacterium abscessus. PNAS NEXUS 2022; 1:pgac130. [PMID: 36714853 PMCID: PMC9802118 DOI: 10.1093/pnasnexus/pgac130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 08/05/2022] [Indexed: 02/01/2023]
Abstract
Infections caused by Mycobacterium abscessus are difficult to treat due to its intrinsic resistance to most antibiotics. Formation of biofilms and the capacity of M. abscessus to survive inside host phagocytes further complicate eradication. Herein, we explored whether addition of a carbamate-linked group at the C25 position of rifamycin SV blocks enzymatic inactivation by ArrMab, an ADP-ribosyltransferase conferring resistance to rifampicin (RMP). Unlike RMP, 5j, a benzyl piperidine rifamycin derivative with a morpholino substituted C3 position and a naphthoquinone core, is not modified by purified ArrMab. Additionally, we show that the ArrMab D82 residue is essential for catalytic activity. Thermal profiling of ArrMab in the presence of 5j, RMP, or rifabutin shows that 5j does not bind to ArrMab. We found that the activity of 5j is comparable to amikacin against M. abscessus planktonic cultures and pellicles. Critically, 5j also exerts potent antimicrobial activity against M. abscessus in human macrophages and shows synergistic activity with amikacin and azithromycin.
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Affiliation(s)
| | | | | | | | - Nhi Van
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, MA 02111, USA
| | - Yonatan Degefu
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, MA 02111, USA
| | - Sonja Staack
- European Molecular Biology Laboratory, 22607 Hamburg, Germany
| | - Flor Vasquez Sotomayor
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Leibniz Lung Center, 23845 Borstel, Germany,Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Lucia Asar
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Holger Rohde
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Bree B Aldridge
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine and Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Boston, MA 02111, USA
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Annabel Parret
- European Molecular Biology Laboratory, 22607 Hamburg, Germany,Charles River Laboratories, 2340 Beerse, Belgium
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, 22607 Hamburg, Germany,University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Laurent Kremer
- Centre National de la Recherche Scientifique UMR 9004, Institut de Recherche en Infectiologie de Montpellier (IRIM), Université de Montpellier, 34293 Montpellier, France,INSERM, Institut de Recherche en Infectiologie de Montpellier, 34293 Montpellier, France
| | - Keith Combrink
- Department of Chemistry and Biochemistry, Texas A&M International University, Laredo, TX 77843, USA,Department of Chemistry, Blinn College, Bryan Campus, Brenham, TX 77833, USA
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4
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Kanglemycin A Can Overcome Rifamycin Resistance Caused by ADP-Ribosylation by Arr Protein. Antimicrob Agents Chemother 2021; 65:e0086421. [PMID: 34606341 PMCID: PMC8597724 DOI: 10.1128/aac.00864-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rifamycins, such as rifampicin (Rif), are potent inhibitors of bacterial RNA polymerase (RNAP) and are widely used antibiotics. Rifamycin resistance is usually associated with mutations in RNAP that preclude rifamycin binding. However, some bacteria have a type of ADP-ribosyl transferases, Arr, which ADP-ribosylate rifamycin molecules, thus inactivating their antimicrobial activity. Here, we directly show that ADP-ribosylation abolishes inhibition of transcription by rifampicin, the most widely used rifamycin antibiotic. We also show that a natural rifamycin, kanglemycin A (KglA), which has a unique sugar moiety at the ansa chain close to the Arr modification site, does not bind to Arr from Mycobacterium smegmatis and thus is not susceptible to inactivation. We, found, however, that kanglemycin A can still be ADP-ribosylated by the Arr of an emerging pathogen, Mycobacterium abscessus. Interestingly, the only part of Arr that exhibits no homology between the species is the part that sterically clashes with the sugar moiety of kanglemycin A in M. smegmatis Arr. This suggests that M. abscessus has encountered KglA or rifamycin with a similar sugar modification in the course of evolution. The results show that KglA could be an effective antimicrobial against some of the Arr-encoding bacteria.
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5
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Blocking Bacterial Naphthohydroquinone Oxidation and ADP-Ribosylation Improves Activity of Rifamycins against Mycobacterium abscessus. Antimicrob Agents Chemother 2021; 65:e0097821. [PMID: 34228543 PMCID: PMC8370238 DOI: 10.1128/aac.00978-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rifampicin is an effective drug for treating tuberculosis (TB) but is not used to treat Mycobacterium abscessus infections due to poor in vitro activity. While rifabutin, another rifamycin, has better anti-M. abscessus activity, its activity is far from the nanomolar potencies of rifamycins against Mycobacterium tuberculosis. Here, we asked (i) why is rifabutin more active against M. abscessus than rifampicin, and (ii) why is rifabutin's anti-M. abscessus activity poorer than its anti-TB activity? Comparative analysis of naphthoquinone- versus naphthohydroquinone-containing rifamycins suggested that the improved activity of rifabutin over rifampicin is linked to its less readily oxidizable naphthoquinone core. Although rifabutin is resistant to bacterial oxidation, metabolite and genetic analyses showed that this rifamycin is metabolized by the ADP-ribosyltransferase ArrMab like rifampicin, preventing it from achieving the nanomolar activity that it displays against M. tuberculosis. Based on the identified dual mechanism of intrinsic rifamycin resistance, we hypothesized that rifamycins more potent than rifabutin should contain the molecule's naphthoquinone core plus a modification that blocks ADP-ribosylation at its C-23. To test these predictions, we performed a blinded screen of a diverse collection of 189 rifamycins and identified two molecules more potent than rifabutin. As predicted, these compounds contained both a more oxidatively resistant naphthoquinone core and C-25 modifications that blocked ADP-ribosylation. Together, this work revealed dual bacterial metabolism as the mechanism of intrinsic resistance of M. abscessus to rifamycins and provides proof of concept for the repositioning of rifamycins for M. abscessus disease by developing derivatives that resist both bacterial oxidation and ADP-ribosylation.
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6
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Novel Ansa-Chain Conformation of a Semi-Synthetic Rifamycin Prepared Employing the Alder-Ene Reaction: Crystal Structure and Absolute Stereochemistry. CHEMISTRY 2021. [DOI: 10.3390/chemistry3030052] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Rifamycins are an extremely important class of antibacterial agents whose action results from the inhibition of DNA-dependent RNA synthesis. A special arrangement of unsubstituted hydroxy groups at C21 and C23, with oxygen atoms at C1 and C8 is essential for activity. Moreover, it is known that the antibacterial action of rifamycin is lost if either of the two former hydroxy groups undergo substitution and are no longer free to act in enzyme inhibition. In the present work, we describe the successful use of an Alder-Ene reaction between Rifamycin O, 1 and diethyl azodicarboxylate, yielding 2, which was a targeted introduction of a relatively bulky group close to C21 to protect its hydroxy group. Many related azo diesters were found to react analogously, giving one predominant product in each case. To determine unambiguously the stereochemistry of the Alder-Ene addition process, a crystalline zwitterionic derivative 3 of the diethyl azodicarboxylate adduct 2 was prepared by reductive amination at its spirocyclic centre C4. The adduct, as a mono chloroform solvate, crystallized in the non-centrosymmetric Sohnke orthorhombic space group, P212121. The unique conformation and absolute stereochemistry of 3 revealed through X-ray crystal structure analysis is described.
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7
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Surur AS, Sun D. Macrocycle-Antibiotic Hybrids: A Path to Clinical Candidates. Front Chem 2021; 9:659845. [PMID: 33996753 PMCID: PMC8120311 DOI: 10.3389/fchem.2021.659845] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/15/2021] [Indexed: 12/21/2022] Open
Abstract
The tale of abate in antibiotics continued defense mechanisms that chaperone the rise of drug-defying superbugs—on the other hand, the astray in antibacterial drug discovery and development. Our salvation lies in circumventing the genesis of resistance. Considering the competitive advantages of antibacterial chemotherapeutic agents equipped with multiple warheads against resistance, the development of hybrids has rejuvenated. The adoption of antibiotic hybrid paradigm to macrocycles has advanced novel chemical entities to clinical trials. The multi-targeted TD-1792, for instance, retained potent antibacterial activities against multiple strains that are resistant to its constituent, vancomycin. Moreover, the antibiotic conjugation of rifamycins has provided hybrid clinical candidates with desirable efficacy and safety profiles. In 2020, the U.S. FDA has granted an orphan drug designation to TNP-2092, a conjugate of rifamycin and fluoroquinolone, for the treatment of prosthetic joint infections. DSTA4637S is a pioneer antibacterial agent under clinical development and represents a novel class of bacterial therapy, that is, antibody–antibiotic conjugates. DSTA4637S is effective against the notorious persistent S. aureus bacteremia, a revelation of the abracadabra potential of antibiotic hybrid approaches.
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Affiliation(s)
- Abdrrahman Shemsu Surur
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, HI, United States
| | - Dianqing Sun
- Department of Pharmaceutical Sciences, The Daniel K. Inouye College of Pharmacy, University of Hawai'i at Hilo, Hilo, HI, United States
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8
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Rifabutin Is Inactivated by Mycobacterium abscessus Arr. Antimicrob Agents Chemother 2021; 65:AAC.02215-20. [PMID: 33318008 DOI: 10.1128/aac.02215-20] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/03/2020] [Indexed: 01/08/2023] Open
Abstract
Mycobacterium abscessus exhibits Arr (ADP-ribosyltransferase)-dependent rifampin resistance. In apparent contrast, rifabutin (RBT) has demonstrated promising activity in M. abscessus infection models, implying that RBT might not be inactivated by Arr. RBT susceptibility testing of M. abscessus Δarr revealed a strongly decreased MIC. Our findings suggest that the efficacy of RBT might be enhanced by rendering RBT resilient to Arr-dependent modification or by blocking M. abscessus Arr activity.
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9
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Faulkner V, Cox AA, Goh S, van Bohemen A, Gibson AJ, Liebster O, Wren BW, Willcocks S, Kendall SL. Re-sensitization of Mycobacterium smegmatis to Rifampicin Using CRISPR Interference Demonstrates Its Utility for the Study of Non-essential Drug Resistance Traits. Front Microbiol 2021; 11:619427. [PMID: 33597931 PMCID: PMC7882622 DOI: 10.3389/fmicb.2020.619427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/21/2020] [Indexed: 12/24/2022] Open
Abstract
A greater understanding of the genes involved in antibiotic resistance in Mycobacterium tuberculosis (Mtb) is necessary for the design of improved therapies. Clustered regularly interspaced short palindromic repeat interference (CRISPRi) has been previously utilized in mycobacteria to identify novel drug targets by the demonstration of gene essentiality. The work presented here shows that it can also be usefully applied to the study of non-essential genes involved in antibiotic resistance. The expression of an ADP-ribosyltransferase (Arr) involved in rifampicin resistance in Mycobacterium smegmatis was silenced using CRISPRi and the impact on rifampicin susceptibility was measured. Gene silencing resulted in a decrease in the minimum inhibitory concentration (MIC) similar to that previously reported in an arr deletion mutant. There is contradictory evidence for the toxicity of Streptococcus pyogenes dCas9 (dCas9Spy) in the literature. In this study the expression of dCas9Spy in M. smegmatis showed no impact on viability. Silencing was achieved with concentrations of the aTc inducer lower than previously described and with shorter induction times. Finally, designing small guide RNAs (sgRNAs) that target transcription initiation, or the early stages of elongation had the most impact on rifampicin susceptibility. This study demonstrates that CRISPRi based gene silencing can be as impactful as gene deletion for the study of non-essential genes and further contributes to the knowledge on the design and induction of sgRNAs for CRISPRi. This approach can be applied to other non-essential antimicrobial resistance genes such as drug efflux pumps.
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Affiliation(s)
- Valwynne Faulkner
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
| | - Adrienne Adele Cox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Shan Goh
- Department of Clinical, Pharmaceutical & Biological Science, School of Life & Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Annelies van Bohemen
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
| | - Amanda J Gibson
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom.,Centre of Excellence for Bovine TB, Aberystwyth University, Aberystwyth, United Kingdom
| | - Oliver Liebster
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
| | - Brendan W Wren
- Department of Infection Biology, The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sam Willcocks
- Department of Infection Biology, The London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Sharon L Kendall
- Pathobiology and Population Sciences, The Royal Veterinary College, Hatfield, United Kingdom
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10
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Mosaei H, Zenkin N. Inhibition of RNA Polymerase by Rifampicin and Rifamycin-Like Molecules. EcoSal Plus 2020; 9:10.1128/ecosalplus.ESP-0017-2019. [PMID: 32342856 PMCID: PMC11168578 DOI: 10.1128/ecosalplus.esp-0017-2019] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Indexed: 12/16/2022]
Abstract
RNA polymerases (RNAPs) accomplish the first step of gene expression in all living organisms. However, the sequence divergence between bacterial and human RNAPs makes the bacterial RNAP a promising target for antibiotic development. The most clinically important and extensively studied class of antibiotics known to inhibit bacterial RNAP are the rifamycins. For example, rifamycins are a vital element of the current combination therapy for treatment of tuberculosis. Here, we provide an overview of the history of the discovery of rifamycins, their mechanisms of action, the mechanisms of bacterial resistance against them, and progress in their further development.
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Affiliation(s)
- Hamed Mosaei
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Newcastle Upon Tyne, NE2 4AX, UK
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11
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Hanh BTB, Park JW, Kim TH, Kim JS, Yang CS, Jang K, Cui J, Oh DC, Jang J. Rifamycin O, An Alternative Anti- Mycobacterium abscessus Agent. Molecules 2020; 25:molecules25071597. [PMID: 32244387 PMCID: PMC7181020 DOI: 10.3390/molecules25071597] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium abscessus is the most difficult-to-treat nontuberculous mycobacteria because of its resistance to many antibiotics. In this study, we screened the Korea Chemical Bank library for a bioluminescent reporter assay to identify molecules capable of acting against M. abscessus. On application of the assay, rifamycin O showed excellent in vitro activity with a narrow range of the minimum inhibitory concentration required to inhibit the growth of 90% of the bacterium (MIC90 = 4.0-6.2 μM); its in vivo efficacy in the zebrafish (Danio rerio) infection model was comparable to that of rifabutin at 25 μM. Furthermore, rifamycin O did not show significant toxicity in cells and the zebrafish model. These results are the first in vivo indication that rifamycin O may be a drug candidate for treating M. abscessus infections.
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Affiliation(s)
- Bui Thi Bich Hanh
- Molecular Mechanisms of Antibiotics, Division of Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea; (B.T.B.H.); (T.H.K.)
- Division of Applied Life Science (BK21plus Program), Gyeongsang National University, Jinju 52828, Korea
| | - June-Woo Park
- Environmental Biology Research Group, Korea Institute of Toxicology, Jinju 52834, Korea;
- Human and Environmental Toxicology Program, Korea University of Science and Technology (UST), Daejeon 34113, Korea
| | - Tae Ho Kim
- Molecular Mechanisms of Antibiotics, Division of Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea; (B.T.B.H.); (T.H.K.)
- Division of Applied Life Science (BK21plus Program), Gyeongsang National University, Jinju 52828, Korea
| | - Jae-Sung Kim
- Department of Bionano Technology, Hanyang University, Seoul 04763, Korea; (J.-S.K.); (C.-S.Y.)
- Department of Molecular & Life Science, Hanyang University, Ansan 15588, Korea
| | - Chul-Su Yang
- Department of Bionano Technology, Hanyang University, Seoul 04763, Korea; (J.-S.K.); (C.-S.Y.)
- Department of Molecular & Life Science, Hanyang University, Ansan 15588, Korea
| | - Kiseok Jang
- Department of Pathology, Hanyang University College of Medicine, Seoul 04763, Korea;
| | - Jinsheng Cui
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (D.-C.O.)
| | - Dong-Chan Oh
- Natural Products Research Institute, College of Pharmacy, Seoul National University, Seoul 08826, Korea; (J.C.); (D.-C.O.)
| | - Jichan Jang
- Molecular Mechanisms of Antibiotics, Division of Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Korea; (B.T.B.H.); (T.H.K.)
- Division of Applied Life Science (BK21plus Program), Gyeongsang National University, Jinju 52828, Korea
- Correspondence: ; Tel.: +82-(0)55-772-1368
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12
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Combrink KD, Ramos AR, Spring S, Schmidl S, Elizondo K, Morin P, De Jesus B, Maurer FP. Rifamycin derivatives active against pathogenic rapidly-growing mycobacteria. Bioorg Med Chem Lett 2019; 29:2112-2115. [PMID: 31281018 DOI: 10.1016/j.bmcl.2019.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/28/2019] [Accepted: 07/01/2019] [Indexed: 11/15/2022]
Abstract
Infections due to rapidly growing mycobacteria (RGM), and in particular the RGM species Mycobacterium abscessus (Mab), are very difficult to treat and reports on novel therapeutic options are scarce. A hallmark of all pathogenic RGM species is their resistance to the four first-line drugs used to treat infections with Mycobacterium tuberculosis including rifampicin. This study demonstrates that modification of the rifampicin scaffold can restore rifampicin activity against the three most commonly isolated pathogenic RGM species including Mab. We also note that the structure-activity relationship for Mab is different as compared to the non-pathogenic RGM species Mycobacterium smegmatis.
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Affiliation(s)
- Keith D Combrink
- Department of Biology and Chemistry, Texas A&M International University, Laredo, USA.
| | - Andrea Ramirez Ramos
- Department of Biology and Chemistry, Texas A&M International University, Laredo, USA
| | - Stephanie Spring
- Department of Biology and Chemistry, Texas A&M International University, Laredo, USA
| | - Sebastian Schmidl
- Department of Biology and Chemistry, Texas A&M International University, Laredo, USA
| | - Kira Elizondo
- Department of Biology and Chemistry, Texas A&M International University, Laredo, USA
| | - Petronilo Morin
- Department of Biology and Chemistry, Texas A&M International University, Laredo, USA
| | - Bryant De Jesus
- Department of Biology and Chemistry, Texas A&M International University, Laredo, USA
| | - Florian P Maurer
- National and WHO Supranational Reference Laboratory for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Ganapathy US, Dartois V, Dick T. Repositioning rifamycins for Mycobacterium abscessus lung disease. Expert Opin Drug Discov 2019; 14:867-878. [PMID: 31195849 DOI: 10.1080/17460441.2019.1629414] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Introduction: The treatment of Mycobacterium abscessus lung disease faces significant challenges due to intrinsic antibiotic resistance. New drugs are needed to cure this incurable disease. The key anti-tubercular rifamycin, rifampicin, suffers from low potency against M. abscessus and is not used clinically. Recently, another member of the rifamycin class, rifabutin, was shown to be active against the opportunistic pathogen. Areas covered: In this review, the authors discuss the rifamycins as a reemerging drug class for treating M. abscessus infections. The authors focus on the differential potency of rifampicin and rifabutin against M. abscessus in the context of intrinsic antibiotic resistance and bacterial uptake and metabolism. Reports of rifamycin-based drug synergies and rifamycin potentiation by host-directed therapy are evaluated. Expert opinion: While repurposing rifabutin for M. abscessus lung disease may provide some immediate relief, the repositioning (chemical optimization) of rifamycins offers long-term potential for improving clinical outcomes. Repositioning will require a multifaceted approach involving renewed screening of rifamycin libraries, medicinal chemistry to improve 'bacterial cell pharmacokinetics', better models of bacterial pathophysiology and infection, and harnessing of drug synergies and host-directed therapy towards the development of a better drug regimen.
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Affiliation(s)
- Uday S Ganapathy
- a Center for Discovery and Innovation, Hackensack Meridian Health , Nutley , NJ , USA
| | - Véronique Dartois
- a Center for Discovery and Innovation, Hackensack Meridian Health , Nutley , NJ , USA
| | - Thomas Dick
- a Center for Discovery and Innovation, Hackensack Meridian Health , Nutley , NJ , USA
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14
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Sun J, Zhu D, Xu J, Jia R, Chen S, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Liu Y, Zhang L, Yu Y, You Y, Wang M, Cheng A. Rifampin resistance and its fitness cost in Riemerella anatipestifer. BMC Microbiol 2019; 19:107. [PMID: 31122209 PMCID: PMC6533769 DOI: 10.1186/s12866-019-1478-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 05/07/2019] [Indexed: 11/25/2022] Open
Abstract
Background Riemerella anatipestifer (R. anatipestifer) is one of the most important poultry pathogens worldwide, with associated infections causing significant economic losses. Rifampin Resistance is an important mechanism of drug resistance. However, there is no information about rpoB mutations conferring rifampin resistance and its fitness cost in Riemerella anatipestifer. Results Comparative analysis of 18 R.anatipestifer rpoB sequences and the determination of rifampin minimum inhibitory concentrations showed that five point mutations, V382I, H491N, G502K, R494K and S539Y, were related to rifampin resistance. Five overexpression strains were constructed using site-directed mutagenesis to validate these sites. To investigate the origin and fitness costs of the rpoB mutations, 15 types of rpoB mutations were isolated from R. anatipestifer ATCC 11845 by using spontaneous mutation in which R494K was identical to the type of mutation detected in the isolates. The mutation frequency of the rpoB gene was calculated to be 10− 8. A total of 98.8% (247/250) of the obtained mutants were located in cluster I of the rifampin resistance-determining region of the rpoB gene. With the exception of D481Y, I537N and S539F, the rifampin minimum inhibitory concentrations of the remaining mutants were at least 64 μg/mL. The growth performance and competitive experiments of the mutant strains in vitro showed that H491D and 485::TAA exhibit growth delay and severely impaired fitness. Finally, the colonization abilities and sensitivities of the R494K and H491D mutants were investigated. The sensitivity of the two mutants to hydrogen peroxide (H2O2) and sodium nitroprusside (SNP) increased compared to the parental strain. The number of live colonies colonized by the two mutants in the duckling brain and trachea were lower than that of the parental strain within 24 h. Conclusions Mutations of rpoB gene in R. anatipestifer mediate rifampin resistance and result in fitness costs. And different single mutations confer different levels of fitness costs. Our study provides, to our knowledge, the first estimates of the fitness cost associated with the R. anatipestifer rifampin resistance in vitro and in vivo. Electronic supplementary material The online version of this article (10.1186/s12866-019-1478-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jiakai Sun
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan, Agricultural University, Chengdu, 611130, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan, Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Jinge Xu
- Guizhou Animal Husbandry and Veterinary Research Institute, Guiyang, 550005, Guizhou, China
| | - Renyong Jia
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan, Agricultural University, Chengdu, 611130, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Shun Chen
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan, Agricultural University, Chengdu, 611130, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Mafeng Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan, Agricultural University, Chengdu, 611130, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Xinxin Zhao
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan, Agricultural University, Chengdu, 611130, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Qiao Yang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan, Agricultural University, Chengdu, 611130, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Ying Wu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan, Agricultural University, Chengdu, 611130, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Shaqiu Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan, Agricultural University, Chengdu, 611130, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China
| | - Yunya Liu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan, Agricultural University, Chengdu, 611130, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ling Zhang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan, Agricultural University, Chengdu, 611130, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yanling Yu
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan, Agricultural University, Chengdu, 611130, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yu You
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan, Agricultural University, Chengdu, 611130, Sichuan, China.,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Mingshu Wang
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan, Agricultural University, Chengdu, 611130, Sichuan, China. .,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China. .,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China.
| | - Anchun Cheng
- Research Center of Avian Diseases, College of Veterinary Medicine, Sichuan, Agricultural University, Chengdu, 611130, Sichuan, China. .,Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China. .,Key Laboratory of Animal Disease and Human Health of Sichuan Province, Chengdu, 611130, Sichuan, China.
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15
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Malík I, Csöllei J, Solovič I, Pospíšilová Š, Michnová H, Jampílek J, Čížek A, Kapustíková I, Čurillová J, Pecháčová M, Stolaříková J, Pecher D, Oravec M. Dibasic Derivatives of Phenylcarbamic Acid against Mycobacterial Strains: Old Drugs and New Tricks? Molecules 2018; 23:E2493. [PMID: 30274224 PMCID: PMC6222509 DOI: 10.3390/molecules23102493] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 12/11/2022] Open
Abstract
In order to provide a more detailed view on the structure⁻antimycobacterial activity relationship (SAR) of phenylcarbamic acid derivatives containing two centers of protonation, 1-[2-[({[2-/3-(alkoxy)phenyl]amino}carbonyl)oxy]-3-(dipropylammonio)propyl]pyrrolidinium oxalates (1a⁻d)/dichlorides (1e⁻h) as well as 1-[2-[({[2-/3-(alkoxy)phenyl]amino}carbonyl)oxy]-3-(di-propylammonio)propyl]azepanium oxalates (1i⁻l)/dichlorides (1m⁻p; alkoxy = butoxy to heptyloxy) were physicochemically characterized by estimation of their surface tension (γ; Traube's stalagmometric method), electronic features (log ε; UV/Vis spectrophotometry) and lipophilic properties (log kw; isocratic RP-HPLC) as well. The experimental log kw dataset was studied together with computational logarithms of partition coefficients (log P) generated by various methods based mainly on atomic or combined atomic and fragmental principles. Similarities and differences between the experimental and in silico lipophilicity descriptors were analyzed by unscaled principal component analysis (PCA). The in vitro activity of compounds 1a⁻p was inspected against Mycobacterium tuberculosis CNCTC My 331/88 (identical with H37Rv and ATCC 2794, respectively), M. tuberculosis H37Ra ATCC 25177, M. kansasii CNCTC My 235/80 (identical with ATCC 12478), the M. kansasii 6509/96 clinical isolate, M. kansasii DSM 44162, M. avium CNCTC My 330/80 (identical with ATCC 25291), M. smegmatis ATCC 700084 and M. marinum CAMP 5644, respectively. In vitro susceptibility of the mycobacteria to reference drugs isoniazid, ethambutol, ofloxacin or ciprofloxacin was tested as well. A very unique aspect of the research was that many compounds from the set 1a⁻p were highly efficient almost against all tested mycobacteria. The most promising derivatives showed MIC values varied from 1.9 μM to 8 μM, which were lower compared to those of used standards, especially if concerning ability to fight M. tuberculosis H37Ra ATCC 25177, M. kansasii DSM 44162 or M. avium CNCTC My 330/80. Current in vitro biological assays and systematic SAR studies based on PCA approach as well as fitting procedures, which were supported by relevant statistical descriptors, proved that the compounds 1a⁻p represented a very promising molecular framework for development of 'non-traditional' but effective antimycobacterial agents.
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Affiliation(s)
- Ivan Malík
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
| | - Jozef Csöllei
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences in Brno, Palackého 1946/1, CZ-612 42 Brno, Czech Republic.
| | - Ivan Solovič
- Clinic for Tuberculosis and Lung Diseases, National Institute for Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, SK-059 84 Vysoké Tatry, Slovakia.
- Department of Public Health, Faculty of Health, Catholic University in Ružomberok, Hrabovská cesta 1A, SK-034 01 Ružomberok, Slovakia.
| | - Šárka Pospíšilová
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
| | - Hana Michnová
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
| | - Josef Jampílek
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
| | - Alois Čížek
- Clinic for Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences, Palackého 1946/1, CZ-612 42 Brno, Czech Republic.
| | - Iva Kapustíková
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
| | - Jana Čurillová
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
| | - Mária Pecháčová
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
| | - Jiřina Stolaříková
- Laboratory for Mycobacterial Diagnostics and Tuberculosis, Regional Institute of Public Health, Partyzánské náměstí 7, CZ-702 00 Ostrava, Czech Republic.
| | - Daniel Pecher
- Department of Pharmaceutical Analysis and Nuclear Pharmacy, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
- Toxicological and Antidoping Center, Faculty of Pharmacy, Comenius University in Bratislava, Odbojárov 10, SK-832 32 Bratislava, Slovakia.
| | - Michal Oravec
- Global Change Research Institute CAS, Belidla 986/4a, CZ-603 00 Brno, Czech Republic.
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16
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Rifabutin Is Active against Mycobacterium abscessus Complex. Antimicrob Agents Chemother 2017; 61:AAC.00155-17. [PMID: 28396540 PMCID: PMC5444174 DOI: 10.1128/aac.00155-17] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/31/2017] [Indexed: 12/30/2022] Open
Abstract
Lung infections caused by Mycobacterium abscessus are emerging as a global threat to individuals with cystic fibrosis and to other patient groups. Recent evidence for human-to-human transmission worsens the situation. M. abscessus is an intrinsically multidrug-resistant pathogen showing resistance to even standard antituberculosis drugs, such as rifampin. Here, our objective was to identify existing drugs that may be employed for the treatment of M. abscessus lung disease. A collection of more than 2,700 approved drugs was screened at a single-point concentration against an M. abscessus clinical isolate. Hits were confirmed with fresh solids in dose-response experiments. For the most attractive hit, growth inhibition and bactericidal activities against reference strains of the three M. abscessus subspecies and a collection of clinical isolates were determined. Surprisingly, the rifampin derivative rifabutin had MICs of 3 ± 2 μM (3 μg/ml) against the screening strain, the reference strains M. abscessus subsp. abscessus ATCC 19977, M. abscessus subsp. bolletii CCUG 50184-T, and M. abscessus subsp. massiliense CCUG 48898-T, as well as against a collection of clinical isolates. Furthermore, rifabutin was active against clarithromycin-resistant strains. In conclusion, rifabutin, in contrast to rifampin, is active against the Mycobacterium abscessus complex bacteria in vitro and may be considered for treatment of M. abscessus lung disease.
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17
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Rominski A, Roditscheff A, Selchow P, Böttger EC, Sander P. Intrinsic rifamycin resistance ofMycobacterium abscessusis mediated by ADP-ribosyltransferase MAB_0591. J Antimicrob Chemother 2016; 72:376-384. [DOI: 10.1093/jac/dkw466] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 09/29/2016] [Accepted: 10/03/2016] [Indexed: 11/14/2022] Open
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18
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Ma Z, Lynch AS. Development of a Dual-Acting Antibacterial Agent (TNP-2092) for the Treatment of Persistent Bacterial Infections. J Med Chem 2016; 59:6645-57. [PMID: 27336583 DOI: 10.1021/acs.jmedchem.6b00485] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The clinical management of prosthetic joint infections and other persistent bacterial infections represents a major unmet medical need. The rifamycins are one of the most potent antibiotic classes against persistent bacterial infections, but bacteria can develop resistance to rifamycins rapidly and the clinical utility of the rifamycin class is typically limited to antibiotic combinations to minimize the development of resistance. To develop a better therapy against persistent bacterial infections, a series of rifamycin based bifunctional molecules were designed, synthesized, and evaluated with the goal to identify a dual-acting drug that maintains the potent activity of rifamycins against persistent pathogens and at the same time minimize the development of rifamycin resistance. TNP-2092 was identified as a drug candidate and is currently in an early stage of clinical development for the treatment of prosthetic joint infections.
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Affiliation(s)
- Zhenkun Ma
- TenNor Therapeutics Ltd. , 218 Xinghu Street, Suzhou Industrial Park, Suzhou 215123, China
| | - Anthony Simon Lynch
- Janssen Research & Development LLC. , 1400 McKean Road, Spring House, Pennsylvania 18940, United States
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19
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Wercholuk AN, Thuman JM, Stanley JL, Sargent AL, Anderson ES, Allen WE. Incorporation of fluorophore-cholesterol conjugates into liposomal and mycobacterial membranes. Bioorg Med Chem 2016; 24:1045-9. [PMID: 26827139 DOI: 10.1016/j.bmc.2016.01.030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 01/05/2016] [Accepted: 01/17/2016] [Indexed: 02/05/2023]
Abstract
Fluorescently-labeled steroids that emit intense blue light in nonpolar solvent (λem (CH2Cl2)≈440nm, ΦF=0.70) were prepared by treating cholesteryl chloroformate with 4-amino-1,8-naphthalimides. The lipid portion of the conjugates embeds into liposomal membrane bilayers in minutes, leaving the fluorophore exposed to the external aqueous environment. This causes a 40-nm red-shift in λem and significant quenching. DFT optimizations predict the conjugates to be about 30Å long when fully extended, but rotation about the linker group can bring the compounds into an 'L'-shape. Such a conformation would allow the cholesteryl anchor to remain parallel to the acyl chains of a membrane while the fluorescent group resides in the interfacial region, instead of extending beyond it. When incubated with Mycobacterium smegmatis mc2 155, a bacterial species known to use natural cholesterol, the labeled steroids support growth and can be found localized in the membrane fraction of the cells using HPLC. These findings demonstrate stable integration of fluorescent cholesterols into bacterial membranes in vivo, indicating that these compounds may be useful for evaluating cholesterol uptake in prokaryotic organisms.
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Affiliation(s)
- Ashley N Wercholuk
- Department of Chemistry, Science and Technology Building, East Carolina University, Greenville, NC 27858-4353, USA; Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858-4353, USA
| | - Jenna M Thuman
- Department of Chemistry, Science and Technology Building, East Carolina University, Greenville, NC 27858-4353, USA; Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858-4353, USA
| | - Jordan L Stanley
- Department of Chemistry, Science and Technology Building, East Carolina University, Greenville, NC 27858-4353, USA; Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858-4353, USA
| | - Andrew L Sargent
- Department of Chemistry, Science and Technology Building, East Carolina University, Greenville, NC 27858-4353, USA; Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858-4353, USA
| | - Eric S Anderson
- Department of Chemistry, Science and Technology Building, East Carolina University, Greenville, NC 27858-4353, USA; Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858-4353, USA
| | - William E Allen
- Department of Chemistry, Science and Technology Building, East Carolina University, Greenville, NC 27858-4353, USA; Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858-4353, USA.
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A rifamycin inactivating phosphotransferase family shared by environmental and pathogenic bacteria. Proc Natl Acad Sci U S A 2014; 111:7102-7. [PMID: 24778229 DOI: 10.1073/pnas.1402358111] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many environmental bacteria are multidrug-resistant and represent a reservoir of ancient antibiotic resistance determinants, which have been linked to genes found in pathogens. Exploring the environmental antibiotic resistome, therefore, reveals the diversity and evolution of antibiotic resistance and also provides insight into the vulnerability of clinically used antibiotics. In this study, we describe the identification of a highly conserved regulatory motif, the rifampin (RIF) -associated element (RAE), which is found upstream of genes encoding RIF-inactivating enzymes from a diverse collection of actinomycetes. Using gene expression assays, we confirmed that the RAE is involved in RIF-responsive regulation. By using the RAE as a probe for new RIF-associated genes in several actinomycete genomes, we identified a heretofore unknown RIF resistance gene, RIF phosphotransferase (rph). The RPH enzyme is a RIF-inactivating phosphotransferase and represents a new protein family in antibiotic resistance. RPH orthologs are widespread and found in RIF-sensitive bacteria, including Bacillus cereus and the pathogen Listeria monocytogenes. Heterologous expression and in vitro enzyme assays with purified RPHs from diverse bacterial genera show that these enzymes are capable of conferring high-level resistance to a variety of clinically used rifamycin antibiotics. This work identifies a new antibiotic resistance protein family and reinforces the fact that the study of resistance in environmental organisms can serve to identify resistance elements with relevance to pathogens.
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21
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Characterization of a rifampin-inactivating glycosyltransferase from a screen of environmental actinomycetes. Antimicrob Agents Chemother 2012; 56:5061-9. [PMID: 22802246 DOI: 10.1128/aac.01166-12] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Identifying and understanding the collection of all antibiotic resistance determinants presented in the global microbiota, the antibiotic resistome, provides insight into the evolution of antibiotic resistance and critical information for the development of future antimicrobials. The rifamycins are broad-spectrum antibiotics that target bacterial transcription by inhibition of RNA polymerase. Although mutational alteration of the drug target is the predominant mechanism of resistance to this family of antibiotics in the clinic, a number of diverse inactivation mechanisms have also been reported. In this report, we investigate a subset of environmental rifampin-resistant actinomycete isolates and identify a diverse collection of rifampin inactivation mechanisms. We describe a single isolate, WAC1438, capable of inactivating rifampin by glycosylation. A draft genome sequence of WAC1438 (most closely related to Streptomyces speibonae, according to a 16S rRNA gene comparison) was assembled, and the associated rifampin glycosyltransferase open reading frame, rgt1438, was identified. The role of rgt1438 in rifampin resistance was confirmed by its disruption in the bacterial chromosome, resulting in a loss of antibiotic inactivation and a 4-fold decrease in MIC. Interestingly, examination of the RNA polymerase β-subunit sequence of WAC1438 suggests that it harbors a resistant target and thus possesses dual mechanisms of rifamycin resistance. Using an in vitro assay with purified enzyme, Rgt1438 could inactivate a variety of rifamycin antibiotics with comparable steady-state kinetics constants. Our results identify rgt1438 as a rifampin resistance determinant from WAC1438 capable of inactivating an assortment of rifamycins, adding a new element to the rifampin resistome.
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22
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23
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Kirst HA. Recent derivatives from smaller classes of fermentation-derived antibacterials. Expert Opin Ther Pat 2011; 22:15-35. [DOI: 10.1517/13543776.2012.642370] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Aristoff PA, Garcia GA, Kirchhoff PD, Showalter HD. Rifamycins--obstacles and opportunities. Tuberculosis (Edinb) 2010; 90:94-118. [PMID: 20236863 DOI: 10.1016/j.tube.2010.02.001] [Citation(s) in RCA: 130] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Revised: 02/02/2010] [Accepted: 02/02/2010] [Indexed: 11/30/2022]
Abstract
With nearly one-third of the global population infected by Mycobacterium tuberculosis, TB remains a major cause of death (1.7 million in 2006). TB is particularly severe in parts of Asia and Africa where it is often present in AIDS patients. Difficulties in treatment are exacerbated by the 6-9 month treatment times and numerous side effects. There is significant concern about the multi-drug-resistant (MDR) strains of TB (0.5 million MDR-TB cases worldwide in 2006). The rifamycins, long considered a mainstay of TB treatment, were a tremendous breakthrough when they were developed in the 1960's. While the rifamycins display many admirable qualities, they still have a number of shortfalls including: rapid selection of resistant mutants, hepatotoxicity, a flu-like syndrome (especially at higher doses), potent induction of cytochromes P450 (CYP) and inhibition of hepatic transporters. This review of the state-of-the-art regarding rifamycins suggests that it is quite possible to devise improved rifamycin analogs. Studies showing the potential of shortening the duration of treatment if higher doses could be tolerated, also suggest that more potent (or less toxic) rifamycin analogs might accomplish the same end. The improved activity against rifampin-resistant strains by some analogs promises that further work in this area, especially if the information from co-crystal structures with RNA polymerase is applied, should lead to even better analogs. The extensive drug-drug interactions seen with rifampin have already been somewhat ameliorated with rifabutin and rifalazil, and the use of a CYP-induction screening assay should serve to efficiently identify even better analogs. The toxicity due to the flu-like syndrome is an issue that needs effective resolution, particularly for analogs in the rifalazil class. It would be of interest to profile rifalazil and analogs in relation to rifampin, rifapentine, and rifabutin in a variety of screens, particularly those that might relate to hypersensitivity or immunomodulatory processes.
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Tupin A, Gualtieri M, Roquet-Banères F, Morichaud Z, Brodolin K, Leonetti JP. Resistance to rifampicin: at the crossroads between ecological, genomic and medical concerns. Int J Antimicrob Agents 2010; 35:519-23. [PMID: 20185278 DOI: 10.1016/j.ijantimicag.2009.12.017] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2009] [Accepted: 12/22/2009] [Indexed: 11/24/2022]
Abstract
The first antibiotic of the ansamycin family, rifampicin (RIF), was isolated in 1959 and was introduced into therapy in 1962; it is still a first-line agent in the treatment of diseases such as tuberculosis, leprosy and various biofilm-related infections. The antimicrobial activity of RIF is due to its inhibition of bacterial RNA polymerase (RNAP). Most frequently, bacteria become resistant to RIF through mutation of the target; however, this mechanism is not unique. Other mechanisms of resistance have been reported, such as duplication of the target, action of RNAP-binding proteins, modification of RIF and modification of cell permeability. We suggest that several of these alternative resistance strategies could reflect the ecological function of RIF, such as autoregulation and/or signalling to surrounding microorganisms. Very often, resistance mechanisms found in the clinic have an environmental origin. One may ask whether the introduction of the RIF analogues rifaximin, rifalazil, rifapentine and rifabutin in the therapeutic arsenal, together with the diversification of the pathologies treated by these molecules, will diversify the resistance mechanisms of human pathogens against ansamycins.
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Affiliation(s)
- Audrey Tupin
- Université Montpellier 1, Centre d'Etudes d'Agents Pathogènes et Biotechnologies pour la Santé (CPBS), CNRS, UMR 5236, 4 Bd Henri IV, CS 69033, F-34965 Montpellier, Cedex 2, France.
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Hansen CP, Jensen AA, Christensen JK, Balle T, Liljefors T, Frølund B. Novel acetylcholine and carbamoylcholine analogues: development of a functionally selective alpha4beta2 nicotinic acetylcholine receptor agonist. J Med Chem 2009; 51:7380-95. [PMID: 18989912 DOI: 10.1021/jm701625v] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of carbamoylcholine and acetylcholine analogues were synthesized and characterized pharmacologically at neuronal nicotinic acetylcholine receptors (nAChRs). Several of the compounds displayed low nanomolar binding affinities to the alpha4beta2 nAChR and pronounced selectivity for this subtype over alpha3beta4, alpha4beta4, and alpha7 nAChRs. The high nAChR activity of carbamoylcholine analogue 5d was found to reside in its R-enantiomer, a characteristic most likely true for all other compounds in the series. Interestingly, the pronounced alpha4beta2 selectivities exhibited by some of the compounds in the binding assays translated into functional selectivity. Compound 5a was a fairly potent partial alpha4beta2 nAChR agonist with negligible activities at the alpha3beta4 and alpha7 subtypes, thus being one of the few truly functionally selective alpha4beta2 nAChR agonists published to date. Ligand-protein docking experiments using homology models of the amino-terminal domains of alpha4beta2 and alpha3beta4 nAChRs identified residues Val111(beta2)/Ile113(beta4), Phe119(beta2)/Gln121(beta4), and Thr155(alpha4)/Ser150(alpha3) as possible key determinants of the alpha4beta2/alpha3beta4-selectivity displayed by the analogues.
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Affiliation(s)
- Camilla P Hansen
- Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, UniVersitetsparken 2, DK-2100 Copenhagen Ø, Denmark
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Rifamycin antibiotic resistance by ADP-ribosylation: Structure and diversity of Arr. Proc Natl Acad Sci U S A 2008; 105:4886-91. [PMID: 18349144 DOI: 10.1073/pnas.0711939105] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The rifamycin antibiotic rifampin is important for the treatment of tuberculosis and infections caused by multidrug-resistant Staphylococcus aureus. Recent iterations of the rifampin core structure have resulted in new drugs and drug candidates for the treatment of a much broader range of infectious diseases. This expanded use of rifamycin antibiotics has the potential to select for increased resistance. One poorly characterized mechanism of resistance is through Arr enzymes that catalyze ADP-ribosylation of rifamycins. We find that genes encoding predicted Arr enzymes are widely distributed in the genomes of pathogenic and nonpathogenic bacteria. Biochemical analysis of three representative Arr enzymes from environmental and pathogenic bacterial sources shows that these have equally efficient drug resistance capacity in vitro and in vivo. The 3D structure of one of these orthologues from Mycobacterium smegmatis was determined and reveals structural homology with ADP-ribosyltransferases important in eukaryotic biology, including poly(ADP-ribose) polymerases (PARPs) and bacterial toxins, despite no significant amino acid sequence homology with these proteins. This work highlights the extent of the rifamycin resistome in microbial genera with the potential to negatively impact the expanded use of this class of antibiotic.
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